Subject: visualizing Delphi output (electrostatic potential)

From: Vlad Cojocaru <[email-masked]>
Date: Thu, 23 Jan 2003 17:08:51 +0100

Dear Friends,
   I have run Delphi jobs and I got ".phi" files.  I also got from 
Delphi runs a files "data",  "ARCDAT". Could somebody explain very 
shortly something about "data" and "ARCDAT"files? Also I would like to 
visualize the electrostatic potential calculated using VMD, gOPENMOL or 
some other software. Could somebody give some hints about how to do that?

For vmders,
   Is VMD able to do this type of job or shell I use something else? I 
do not have installed Delphi on the machine that I want to visualize the 
data so dont know if the scripts from the library are applicable. All 
that I have is the output files from Delphi.

Thanks a lot in advance for any kind of help,
Best regards,
vlad

-- 
Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
e-mail: [email-masked]
home tel: ++49-551-9963204

---

From: John Stone <[email-masked]>
Date: Thu, 23 Jan 2003 10:23:09 -0600

Dear Vlad,
  There are two VMD scripts available which may be of interest to you
since you have access to Delphi.  One is "potsel" which calculates
potential for an atom selection in VMD, and the other is "potsurf"
which colors a surface representation in VMD by the potential values
supplied by Delphi.  These two scripts should be a good starting point 
for you to get VMD working with Delphi.

The two scripts are here:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsel/
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/potsurf/

Along the same lines, I believe that Nathan Baker's APBS package
comes with some scripts to allow it to work with VMD.
It is available for free, and they've got a web portal setup for 
running jobs on the NPACI machines:
  http://agave.wustl.edu/apbs/

Thanks,
  John Stone
  [email-masked]

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: [email-masked]                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

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From: "Leif Laaksonen" <[email-masked]>
Date: Thu, 23 Jan 2003 20:23:24 +0200

Vlad,

Look into the gOpenMol util/ directory where you find
the delphi2plt program for converting phi files to plt
files for gOpenMol.

Regards,

-leif

-----Original Message-----
From: Computational Chemistry List [mailto:[email-masked]] On Behalf Of Vlad Cojocaru
Sent: Thursday, January 23, 2003 6:09 PM
To: VMD; CCL
Subject: CCL:visualizing Delphi output (electrostatic potential)

Dear Friends,

For vmders,

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